Table 2.
Structure and function of nonstructural proteins of SARS-CoV and SARS-CoV-2.
| Name | Functional name | Structure solved (SARS-CoV-2) | Structure solved (SARS-CoV) | Structure description | Function |
|---|---|---|---|---|---|
| Nsp1 | Virulent factor | Cryo-EM Structure and X-Ray Crystallography structure PDB:7K5I, 7K3 N, 7K7 P | NMR Structure PDB: 2GDT |
The SARS-CoV-2 nsp113-127 like that of SARS-CoV hosts a unique topological arrangement, which gives to the formation of a six-stranded (n = 6) beta-barrel. In addition, there is an alpha1 helix which is positioned as a cap along one opening of the beta-barrel, two 310 helices that run parallel to each other and the beta5 strand which is though not a part of the beta-barrel but forms a beta-sheet interaction with the beta4 strand. As evident in the crystal structure of nsp113 127, nsp1 of SARS-CoV-2 has large number of flexible loops. | It inhibits host translation, causes invasion from host immune response and leads to efficient viral gene expression in infected cells.14,21 |
| Nsp2 | Endosome-associated protein | – | – | N/A | It is entirely unknown. In SARS-CoV-2 as well, the other proteins nsp2 attaches to may offer some clues. Nsp2 interacts with PHB1 and PHB2 host protein complexes, which are involved in mitochondrial biogenesis. 22 |
| Nsp3 | Cutting and untagging protein | X-Ray Crystallography PDB: 6YWL, 6WEY, 6WOJ, 7CZ4, 7CJD, 7C33, 7LLZ, 7LOS, 7CMD, 7JIW,7LLZ | X-Ray Crystallography PDB: 4MM3, | It contains two transmembrane domains, which is released from pp1a/1ab by the papain-like protease domain, which is a part of nsp3 itself. | It releases nsp1 and nsp2 from polyprotein, interacts with other viral nsps as well as RNA to form replication/transcription complex 23 and removes tags from old proteins set for destruction. 24 |
| Nsp4 | Double-membrane vesicle maker | – | – | It is predicted to contain four transmembrane domains, both termini projecting at the cytoplasmic side of the membrane, and three loop regions. | Nsp3, 4, and 6 are predicted to function to nucleate and anchor viral replication complexes on double-membrane vesicles in the cytoplasm.11-13 |
| Nsp5 | Protease (3CLpro) | X-Ray Crystallography PDB: 6M2N, 2M2N, 7L0D, 6M2Q, 7JKV, 7JQ3, 7JPY, 7JPZ, 7JQ0, 7JQ1, 7JQ4, 7JQ5, 7JQ2 | X-Ray Crystallography PDB: 2HOB, 3SN8 | 3CLpro monomer has 3 domains, domain I, domain II, domain III and a long loop. The active site of 3CLpro is located in the gap between domains I and II, and has a CysHis catalytic dyad. | 3CLpro is first automatically cleaved from polyproteins to produce mature enzyme, which then cleaves downstream nsps at 11 sites to release nsp4-nsp16. 15 |
| Nsp6 | Double-membrane vesicle factory | – | – | Nsp6 protein possesses 7 putative transmembrane helices located in endoplasmic reticulum (ER). | Nsp3, 4 and 6 are predicted to function to nucleate and anchor viral replication complexes on double-membrane vesicles in the cytoplasm.11-13 |
| Nsp7 | Copy assistant | Nsp7-nsp8-nsp12 structure solved (X-Ray Crystallography) PDB: 7JLT, 6YHU, 7DCD, 7BW4, 6M71 | Nsp7-nsp8 structure solved (X-Ray Crystallography) PDB: 2AHM | It has a hexadecameric structure with 8 nsp7 and nsp8s that encircles double-stranded RNA. | SARS-CoV nsp7 dimerizes and interacts with other proteins such as nsp5, nsp8, nsp9, and nsp13. 14 |
| Nsp8 | Primase | Nsp7-nsp8-nsp12 structure solved (X-Ray Crystallography) PDB: 7JLT, 6YHU, 7DCD, 7BW4, 6M71 | Nsp7-nsp8 structure solved (X-Ray Crystallography) PDB: 2AHM | It has a hexadecameric structure with 8 nsp7 and nsp8s that encircles double-stranded RNA. | Nsp8 enzyme is able of de novo initiate replication and has been proposed to operate as primase
25
. Nsp8 is known to colocalize with RdRp to copy the SARS-CoV genome. 25 |
| Nsp9 | RNA-binding protein | X-Ray Crystallography PDB: 6WXD | X-Ray Crystallography PDB: 3EE7 | It consists of an unusual fold and its core is made up of 6-stranded enclosed β-barrel and a series of extended loops projects outward from it. | It is a single-stranded RNA-binding protein, which displays an oligosaccharide/oligonucleotide binding fold. 26 |
| Nsp10 | Methyltransferase stimulator | Solved as nsp10-nsp16-SAM complex (X-Ray Crystallography) PDB: 7BQ7, 7JYY | Solved as nsp10-nsp16-SAM complex (X-Ray Crystallography) PDB:3R24 | It comprises a central anti-parallel pair of β-strands, surrounded by a broad crossover loop on one side. On the other side, a helical domain with loops is present, which generates 2 zinc fingers. | It stimulates nsp16 to execute S-adenosyl-L-methionine (SAM)-dependent methyltransferase (MTase) activity 20 |
| Nsp12 | RNA-dependent RNA polymerase | Solved as nsp7-nsp8-nsp12 (Electron Microscopy) PDB: 6M71, 7JLT, 6YHU, 7DCD, 7BW4, 7AAP | Solved as nsp7-nsp8-nsp12 (Electron Microscopy) PDB: 6NUR Solved as nsp7-nsp8 complex (Electron Microscopy) PDB: 6NUS |
It consists of N-terminal and polymerase domain which resembles a cupped “right hand” consisting a finger, a palm, and a thumb subdomain | Nsp12, in association with nsp7, nsp8, and other essential components of the RNA synthesis machinery, forms a viral replication complex. 27 |
| Nsp13 | Helicase | X-Ray Crystallography PDB: 6ZSL, 7NI0, 7NN0, 7NNG | – | Nsp13 adopts a triangular pyramid shape comprising five domains: two “RecA-like” domains (1A and 2A), and 1B domain, N-terminal zinc-binding domain (ZBD) and stalk domain, which connects ZBD and 1B domain. | It unwinds dsRNA or DNA with a 5′→3′ polarity, using energy from nucleotide hydrolysis. 28 |
| Nsp14 | Proofreading exonuclease | – | Nsp14-nsp10 complex solved (X-Ray Crystallography) PDB: 5C8U | The ExoN domain features a core, twisted β-sheet consisting of five β-strands with one Mg2+ ion at its active site. The N7-MTase domain features a MTase fold with central β-sheet consisting of five β-strands. β1 and β2 sheets have a ligand-binding cavity in-between. | Its N-terminal exoribonuclease domain has a proofreading role, which prevents lethal mutagenesis, whereas the C-terminal domain functions as a (guanine-N7) methyltransferase (N7-MTase) for mRNA capping. 29 |
| Nsp15 | Endonuclease | X-Ray Crystallography PDB: 7KEG, 7KEH, 7KF4 | Catalytically inactive mutant version of Nsp15 solved (X-Ray Crystallography) PDB: 2RHB | Nsp15 forms dimers of trimers, which finally assembles into a hexamer. Each subunit consists of N-terminal domain, a middle domain and C-terminal catalytic endonuclease domain. | Nsp15 preferentially cleaves 3′ of uridines in a manganese dependent manner. This is thought to be an important way for the virus to hide from antiviral defense. 30 |
| Nsp16 | Methyltransferase | Solved as nsp10-nsp16-SAM complex (X-Ray Crystallography) PDB: 7BQ7, 7JYY | Solved as nsp10-nsp16-SAM complex (X-Ray Crystallography) PDB:3R24 | It consists of Rossmann-like β-sheet fold surrounded by 11 α-helices, 7 β-strands, and loops in the 2′-O-MTase catalytic core. | Nsp16 recruits N7-methylated capped RNA and SAM which promotes the assembly of the enzymatically active nsp10/nsp16 complex. This complex converts 7mGpppG (cap-0) into 7mGpppG2′Om (cap-1) RNA by 2′-OH methylation of N1. 31 |
Abbreviations: Cryo-EM, cryogenic electron microscopy; DNA, deoxyribonucleic acid; NMR = nuclear magnetic resonance; RdRp, RNA-dependent RNA polymerase; RNA, ribonucleic acid.